New funding from the Broad Next10!

(As is now become somewhat habitual, I’m reporting a week late to get some clarity in thought.) Really humbling and yet exciting week last week. With my colleagues Tony and Jared (Blainey lab) at the Broad, we won a $40,000 Broad Next10 (Bn10) grant to conduct exploratory and hopefully “catalytic” experiments to develop influenza polymerase […]

PyFlatten: A package for flattening nested data structures

Yesterday, I released PyFlatten to PyPI – it’s a utility that can flatten nested data structures (e.g. list of lists; dictionaries of lists of tuples) into a single 1-by-N vector, while also returning an ‘unflattener’ function that can restore the original data structure from the flattened version. The source code are available on GitHub, where I […]

Packaging Python packages for pypi

I just discovered a tool called pipreqs, and it’s embarrassingly easy to use to create a requirements.txt file. To use it, just do: pip install pipreqs pipreqs /path/to/project And that’s it! Of course, then, after uploading it to pypi, don’t forget to upload it to Anaconda Cloud as well! Credit to this webpage.

Recent Papers

Finally, after ~2 years of learning, working, collaborating and writing, there’s been a slew of papers from our research lab going out. Really happy to have finally contributed to our collective scientific knowledge, both through my own efforts and through working with others. Here’s the list of papers, and I’m absolutely thrilled to have contributed […]

Lessons learned from publishing the reassortment paper

The paper can be found here (preprint, freely available; accepted at PNAS and in press). In no order of importance, here are the things I would tell myself to do from the start. Lesson 1. Computational work requires simulated data. Creating simulated data is paramount. Just as writing an idea down for an audience forces […]

The back-story to our publication on influenza reassortment.

For the reader of a newly-published article, all that we see is precisely that – the article itself. We rarely get to hear about the back-story of that paper, or the choices that were made, the struggles involved, and the emotional ride taken. I thought I’d take the time to document what the back-story to […]

Life after Science One: A Journey in Computation and Creativity

Writer’s note: This blog post was written for the class of Science One 2015/2016, 9 years on after my own experience in Science One 2006/2007. My classmate, Jacob Bayless, is giving a talk to them titled “Life After Science One”, and reached out to me for some perspectives on learning computation. Here’s my piece, for […]